I recently got a '96 2wd tacoma to use for running around and because of the abundance of available parts and getting ideas from the Internet I started doing minor mods to it to help with comfort and to get me back into something mechanical which is what I did for a while but have not done recently.
I want to add power windows, not very concerned with locks and really am only concerned with the passenger door at the moment. I know there are aftermarket kits that seam like they would work fine (I think an old Chevy I had my have had a set in it when I got it) and seem reasonably priced but it dosen't seem hard to find complete doors so I was wondering if retrofitting either an entire power door or the power guts would be an alternative. The electric motor looks like it will bolt right in so I was wondering if I did that what governs the motor to shut it off when reaching the top or bottom is it in the motor itself. Also, if I bolted on doors with power windows would I just need to run power to the two doors and connect them together so driver door controls passenger or is there any on board electronics I would need to add (assuming I don't worry about keyless entry).
Thanks seams like it should be simple but I wasn't sure about a few things. Any pointers or links would be great. Mostly concerned with controlling the motor if I added it.

Basically its juts a 3 way switch that tell the motor to turn on and off.

You should be able to just swap doors or swap the internals. I did when i put a 2wd body on to my 4wd frame. All just bolted right in. But i had a wiring harness with the E windows so i didn't have to run new wires. In theory though yes you would just have to get ground and power to the motors/ switch.

I would recomemnd if you can find some tacoma doors with them in to swap the internals or whole door. The manual opener doesnt have a good way of attacthing the motor and i doubt it would work as well as a OEM one.

Its pretty simple to do. Power locks are a PITA to swap in and out just due to space issues.